CDV3

Summary

CDV3 (CDV3 homolog, HGNC:26928) is a protein-coding gene on chromosome 3q22.1, encoding Protein CDV3 homolog (Q9UKY7).

Located in cytosol and plasma membrane.

Source: NCBI Gene 55573 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 43 total
• Druggable target: yes
• MANE Select transcript: NM_017548

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26928
Approved symbol	CDV3
Name	CDV3 homolog
Location	3q22.1
Locus type	gene with protein product
Status	Approved
Aliases	H41
Ensembl gene	ENSG00000091527
Ensembl biotype	protein_coding
OMIM	618789
Entrez	55573

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 nonsense_mediated_decay

ENST00000264993, ENST00000420115, ENST00000431519, ENST00000503932, ENST00000504867, ENST00000507408, ENST00000508481, ENST00000511392, ENST00000515421, ENST00000688838, ENST00000918067, ENST00000946720

RefSeq mRNA: 8 — MANE Select: NM_017548 NM_001134422, NM_001134423, NM_001282762, NM_001282763, NM_001282764, NM_001282765, NM_001410823, NM_017548

CCDS: CCDS3079, CCDS46917, CCDS46918, CCDS75013, CCDS75014, CCDS75015, CCDS93387

Canonical transcript exons

ENST00000264993 — 5 exons

Exon	Start	End
ENSE00001164188	133587896	133590261
ENSE00001346369	133573686	133574284
ENSE00001409725	133586563	133586722
ENSE00003501539	133575039	133575115
ENSE00003786794	133584002	133584150

Expression profiles

Bgee: expression breadth ubiquitous, 302 present calls, max score 99.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 145.8029 / max 867.5153, expressed in 1827 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38657	75.7368	1826
38662	22.7156	1807
38658	18.6095	1800
38655	9.4330	1725
38659	8.1852	1760
38667	3.9420	1436
38656	2.1509	1282
38660	1.6120	1079
38664	0.9940	603
38661	0.9120	583

Top tissues by expression

302 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
parietal pleura	UBERON:0002400	99.31	gold quality
visceral pleura	UBERON:0002401	99.29	gold quality
pleura	UBERON:0000977	99.22	gold quality
cartilage tissue	UBERON:0002418	99.18	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	98.94	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	98.94	gold quality
esophagus squamous epithelium	UBERON:0006920	98.93	gold quality
mucosa of sigmoid colon	UBERON:0004993	98.83	gold quality
germinal epithelium of ovary	UBERON:0001304	98.81	gold quality
gluteal muscle	UBERON:0002000	98.80	gold quality
trabecular bone tissue	UBERON:0002483	98.79	gold quality
corpus epididymis	UBERON:0004359	98.79	gold quality
tendon of biceps brachii	UBERON:0008188	98.79	gold quality
biceps brachii	UBERON:0001507	98.78	gold quality
oral cavity	UBERON:0000167	98.71	gold quality
vastus lateralis	UBERON:0001379	98.67	gold quality
epithelium of esophagus	UBERON:0001976	98.66	gold quality
quadriceps femoris	UBERON:0001377	98.58	gold quality
renal glomerulus	UBERON:0000074	98.50	gold quality
colonic epithelium	UBERON:0000397	98.49	gold quality
heart right ventricle	UBERON:0002080	98.48	gold quality
skeletal muscle tissue	UBERON:0001134	98.47	gold quality
tibia	UBERON:0000979	98.45	gold quality
metanephric glomerulus	UBERON:0004736	98.44	gold quality
bone marrow cell	CL:0002092	98.42	gold quality
tendon	UBERON:0000043	98.42	gold quality
colonic mucosa	UBERON:0000317	98.38	gold quality
squamous epithelium	UBERON:0006914	98.38	gold quality
bone element	UBERON:0001474	98.37	gold quality
monocyte	CL:0000576	98.36	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-79	yes	561.22
E-HCAD-13	yes	8.21
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

85 targeting CDV3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-5696	99.98	72.36	4487
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-9902	99.89	69.15	2250

Literature-anchored findings (GeneRIF, showing 1)

• Differential mRNA display shows increased levels of CDV3 in mice with cardiac hypertrophy. (PMID:12359334)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdv3	ENSDARG00000023028
mus_musculus	Cdv3	ENSMUSG00000032803
rattus_norvegicus	Cdv3	ENSRNOG00000010186
rattus_norvegicus		ENSRNOG00000086256

Protein

Protein identifiers

Protein CDV3 homolog — Q9UKY7 (reviewed: Q9UKY7)

All UniProt accessions (8): Q9UKY7, A0A8I5KX85, D6R973, D6R9V8, D6RAV0, D6RDN0, D6RFH2, H0Y8K3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Tissue specificity. Expression levels correlate with those of HER-2/neu in breast cancer cells.

Similarity. Belongs to the CDV3 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9UKY7-1	1	yes
Q9UKY7-2	2
Q9UKY7-3	3

RefSeq proteins (8): NP_001127894, NP_001127895, NP_001269691, NP_001269692, NP_001269693, NP_001269694, NP_001397752, NP_060018* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026806	CDV3	Family

Pfam: PF15359

UniProt features (22 total): modified residue 9, splice variant 5, compositionally biased region 5, initiator methionine 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UKY7-F1	61.82	0.01

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (9): 8, 95, 106, 107, 182, 190, 244, 2, 4

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 209 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, ELVIDGE_HYPOXIA_DN, MODULE_52, ACTACCT_MIR196A_MIR196B, GNF2_BNIP2, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, MORF_UBE2I, MODULE_16, PUJANA_CHEK2_PCC_NETWORK, MODULE_239, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, ZHAN_MULTIPLE_MYELOMA_HP_UP, MASSARWEH_RESPONSE_TO_ESTRADIOL, SENESE_HDAC1_TARGETS_UP, GNF2_DDX5

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
intracellular anatomical structure	1
cytoplasm	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDV3	AKAP5	P24588	601
CDV3	H2AC19	P20670	590
CDV3	H2AC20	Q16777	590
CDV3	H2BC21	Q16778	569
CDV3	H1-6	P22492	506
CDV3	GOLM2	Q6P4E1	506
CDV3	TMEM108	Q6UXF1	453
CDV3	CFHR1	Q03591	419
CDV3	PRMT3	O60678	400
CDV3	H3-7	Q5TEC6	390
CDV3	BRD4	O60885	375
CDV3	H3-4	Q16695	370
CDV3	H1-8	Q8IZA3	370
CDV3	RPS2	P15880	350
CDV3	NDNF	Q8TB73	349
CDV3	H4C7	Q99525	349

IntAct

34 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
BMI1	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
MYC		psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
HSPA8	AGPS	psi-mi:“MI:0914”(association)	0.350
LMNA	CLIC1	psi-mi:“MI:0914”(association)	0.350
hspa1a_hspa1b_human-1	SHTN1	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
SLC35F4	SHTN1	psi-mi:“MI:0914”(association)	0.350
SLC35G3	SMCHD1	psi-mi:“MI:0914”(association)	0.350
CFTR	UBA6	psi-mi:“MI:2364”(proximity)	0.270
MAPT	PITPNM1	psi-mi:“MI:2364”(proximity)	0.270
MAPT	DCTN6	psi-mi:“MI:2364”(proximity)	0.270
MAPT		psi-mi:“MI:2364”(proximity)	0.270
AGGF1	BLTP3B	psi-mi:“MI:2364”(proximity)	0.270
APOBEC3C	CNOT1	psi-mi:“MI:2364”(proximity)	0.270
DGCR8	VWA8	psi-mi:“MI:2364”(proximity)	0.270
FASTKD2	MED19	psi-mi:“MI:2364”(proximity)	0.270
GPKOW	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
LARP7	SBNO1	psi-mi:“MI:2364”(proximity)	0.270
LIN28B	MEX3A	psi-mi:“MI:2364”(proximity)	0.270
SBDS	RPSA2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (102): CDV3 (Co-fractionation), CDV3 (Co-fractionation), CHMP2A (Co-fractionation), ILK (Co-fractionation), NAA50 (Co-fractionation), NHP2L1 (Co-fractionation), NUP50 (Co-fractionation), PGD (Co-fractionation), PSMD9 (Co-fractionation), UBAP2L (Co-fractionation), CDV3 (Proximity Label-MS), CDV3 (Proximity Label-MS), CDV3 (Affinity Capture-MS), CDV3 (Affinity Capture-MS), CDV3 (Affinity Capture-MS)

ESM2 similar proteins: A4PB26, D3ZTQ1, G1SW77, O16053, O88271, Q12872, Q32LE2, Q3MHS2, Q3U155, Q3USH5, Q4ADK4, Q4ADK7, Q4VAA2, Q5M8L3, Q5PQP2, Q5PQS7, Q5RKH3, Q5VSY0, Q5XHI2, Q5XIG5, Q5XIM5, Q5ZLH9, Q60FC2, Q63ZM9, Q6AXS5, Q6DIS2, Q6DJ13, Q6GNQ4, Q6NWC9, Q6PFK1, Q75UQ2, Q7T370, Q7ZYA6, Q8HXY9, Q8K039, Q8MMC4, Q8NC51, Q8R1N0, Q92733, Q96NB3

Diamond homologs: A4PB26, Q4VAA2, Q5XIM5, Q5ZLH9, Q6DIS2, Q7T370, Q7ZYA6, Q9UKY7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

43 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

901 predictions. Top by Δscore:

Variant	Effect	Δscore
3:133575033:TTACA:T	acceptor_loss	1.0000
3:133575034:TACA:T	acceptor_loss	1.0000
3:133575037:A:AG	acceptor_gain	1.0000
3:133575037:AGGA:A	acceptor_loss	1.0000
3:133575038:G:GG	acceptor_gain	1.0000
3:133575038:G:T	acceptor_loss	1.0000
3:133575111:ATAAG:A	donor_loss	1.0000
3:133575112:TAAG:T	donor_loss	1.0000
3:133575113:AAGGT:A	donor_loss	1.0000
3:133575115:GGTA:G	donor_loss	1.0000
3:133575116:GTAT:G	donor_loss	1.0000
3:133575117:T:A	donor_loss	1.0000
3:133583996:TTCCA:T	acceptor_loss	1.0000
3:133583997:TCCA:T	acceptor_loss	1.0000
3:133583998:CCA:C	acceptor_loss	1.0000
3:133583999:CA:C	acceptor_loss	1.0000
3:133584000:A:AC	acceptor_loss	1.0000
3:133584000:A:AG	acceptor_gain	1.0000
3:133584001:G:GA	acceptor_gain	1.0000
3:133584001:GC:G	acceptor_gain	1.0000
3:133584001:GCA:G	acceptor_gain	1.0000
3:133584001:GCAGT:G	acceptor_gain	1.0000
3:133584144:G:GG	donor_gain	1.0000
3:133574163:G:GT	donor_gain	0.9900
3:133575038:GGAC:G	acceptor_gain	0.9900
3:133575103:C:T	donor_gain	0.9900
3:133583991:T:TA	acceptor_gain	0.9900
3:133583999:CAGCA:C	acceptor_gain	0.9900
3:133584000:AGCAG:A	acceptor_gain	0.9900
3:133584003:AGT:A	acceptor_gain	0.9900

AlphaMissense

1699 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:133574078:T:C	F12L	1.000
3:133574079:T:G	F12C	1.000
3:133574080:C:A	F12L	1.000
3:133574080:C:G	F12L	1.000
3:133574081:T:C	F13L	1.000
3:133574082:T:G	F13C	1.000
3:133574083:T:A	F13L	1.000
3:133574083:T:G	F13L	1.000
3:133574091:G:T	R16M	1.000
3:133575091:T:C	L98P	1.000
3:133584105:T:A	W141R	1.000
3:133584105:T:C	W141R	1.000
3:133584107:G:C	W141C	1.000
3:133584107:G:T	W141C	1.000
3:133586679:T:C	F195L	1.000
3:133586680:T:C	F195S	1.000
3:133586680:T:G	F195C	1.000
3:133586681:C:A	F195L	1.000
3:133586681:C:G	F195L	1.000
3:133587918:T:C	F217L	1.000
3:133587920:T:A	F217L	1.000
3:133587920:T:G	F217L	1.000
3:133574070:T:A	L9Q	0.999
3:133574079:T:C	F12S	0.999
3:133574081:T:A	F13I	0.999
3:133574081:T:G	F13V	0.999
3:133574082:T:C	F13S	0.999
3:133574092:G:C	R16S	0.999
3:133574092:G:T	R16S	0.999
3:133574094:A:T	D17V	0.999

dbSNP variants (sampled 300 via entrez): RS1000072172 (3:133572522 T>C), RS1000129865 (3:133578220 G>A,T), RS1000423489 (3:133572812 A>C,G), RS1000485103 (3:133573450 C>G), RS1000486156 (3:133572341 C>A,T), RS1000591754 (3:133577944 T>G), RS1000645512 (3:133577645 C>CCT), RS1000750541 (3:133583426 T>A), RS1000892124 (3:133576887 G>C,T), RS1001133292 (3:133577074 C>T), RS1001204229 (3:133583269 A>C), RS1001214619 (3:133575592 A>G), RS1001266827 (3:133575350 C>G), RS1001319104 (3:133575121 G>A), RS1001374906 (3:133582546 C>T)

Disease associations

OMIM: gene MIM:618789 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001958_9	Bulimia nervosa	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067284 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.19	Kd	65.13	nM	CHEMBL5653589
7.09	ED50	80.35	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148057: Binding affinity to human CDV3 incubated for 45 mins by Kinobead based pull down assay	kd	0.0651	uM

CTD chemical–gene interactions

60 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, increases expression	4
bisphenol S	decreases methylation, increases expression, affects cotreatment	3
Estradiol	affects cotreatment, decreases expression, increases expression	3
Tobacco Smoke Pollution	affects expression, increases expression	3
perfluorooctanoic acid	affects cotreatment, decreases expression, increases expression	2
Air Pollutants	affects expression, increases abundance, increases expression	2
Cisplatin	affects cotreatment, decreases expression	2
Cyclosporine	increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
deoxynivalenol	increases expression	1
trichostatin A	affects expression	1
arsenite	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	affects cotreatment, decreases expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
bisphenol B	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
bisphenol AF	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	increases expression	1
Arsenic Trioxide	increases expression	1
Acetaminophen	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651099	Binding	Binding affinity to human CDV3 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2U2	Abcam HEK293T CDV3 KO	Transformed cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.